Hi Joseph,
The question for cover is:
a) Does the app/device support embedded covers? and
b) For what device/app/retail store are you targeting? "epub" isn't a good enough qualifier, although "mobi" is because we're presuming that's the file you're sending to Amazon (hence the Kindle).
Here's a website with the breakdown for some of the retailers:
http://www.natashafondren.com/writin...-ipad-formats/